Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins


  • Nickolai N. Alexandrov,

    Corresponding author
    1. Protein Engineering Research Institute, 5–2–3 Furuedai, Suita, Osaka 565, Japan
    • Laboratory of the Mathematical Biology, Building 469, Room 151, FCRF-NCI, Frederick, Maryland 21702; e-mail:
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  • Nobuhiro Gō

    1. Chemistry Department, Faculty of Science, Kyoto University, Kyoto 606, Japan
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We have completed an exhaustive search for the common spatial arrangements of backbone fragments (SARFs) in nonhomologous proteins. This type of local structural similarity, incorporating short fragments of backbone atoms, arranged not necessarily in the same order along the polypeptide chain, appears to be important for protein function and stability. To estimate the statistical significance of the similarities, we have introduced a similarity score. We present several locally similar structures, with a large similarity score, which have not yet been reported. On the basis of the results of pairwise comparison, we have performed hierarchical cluster analysis of protein structures. Our analysis is not limited by comparison of single chains but also includes complex molecules consisting of several subunits. The SARFs with backbone fragments from different polypeptide chains provide a stable interaction between subunits in protein molecules. In many cases the active site of enzymes is located at the same position relative to the common SARFs, implying a function of the certain SARFs as a universal interface of the protein-substrate interaction.